Hi Dan,
thanks for your reply.
Your suggestion seems to be working, now I only have to choose the right residues to use as anchor but the multimeric form now shows to be much better within the water box boundaries.
On a different task, would it make sense to use the RDF function to look for the number of water molecules that get in the different active sites, i. e. the RDF of wat mols around the metal cofactor in the active site? Or the Watershell command is more indicated for the study?
Kind regards,
Damiano
________________________________
Da: Damiano Spadoni <ezads12.exmail.nottingham.ac.uk>
Inviato: martedì 8 novembre 2022 13:35
A: amber.ambermd.org <amber.ambermd.org>
Oggetto: Reimaging issues
Hi AMBERists,
I am having issues in reimaging the MD simulations of a Protein in an orthorombic box of water. I want to check the permeability of the catalytic pocket through the homodimeric structure of the protein, if a different number of water molecules get into the active site of each monomer. To do this I thought to calculate the coordination number of the metal centre in the active site vs. water molecules. You might suggest a different strategy for doing this - am open to suggestions, of course.
My issue comes from the attempts of reimaging the trajectories as I thought water molecules should be included to measure how many of those get into the different pockets. The output coming from my cpptraj script seems to have the water box centred but not the protein, the protein always looks shifted from the centre of the box and there are "cavities" in the water box. My script looks like this:
parm Protein.prmtop
trajin Protein_md10ns.mdcrd 0 last 50
unwrap :1-1640 #the protein is 1640 amino acid long
image origin center :1-1640 familiar
center :1-1640 mass origin
autoimage
trajout Reimaged_trajectories.nc netcdf
Kind regards,
Damiano
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please contact the sender and delete the email and
attachment.
Any views or opinions expressed by the author of this email do not
necessarily reflect the views of the University of Nottingham. Email
communications with the University of Nottingham may be monitored
where permitted by law.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 13 2022 - 12:30:03 PST
